Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-03-12, 13:43 PDT based on data in: /scratch/eanderson/TEST/mega-non-model-wgs-snakeflow/results/bqsr-round-0/qc/fastp


        General Statistics

        Showing 102/102 rows and 5/7 columns.
        Sample Name% DuplicationM Reads After FilteringGC content% PF% Adapter
        M004147_M028_1A_S62_R1_001
        20.4%
        45.5M
        43.0%
        98.0%
        25.5%
        M004182_M028_5D_S61_R1_001
        20.8%
        43.5M
        42.7%
        98.1%
        22.8%
        M004225_M028_10G_S74_R1_001
        22.3%
        22.7M
        43.1%
        98.2%
        12.6%
        M004226_M028_10H_S75_R1_001
        20.5%
        21.4M
        42.3%
        97.9%
        13.1%
        M004444_M031_2B_S30_R1_001
        20.1%
        25.9M
        42.6%
        97.7%
        10.6%
        M004446_M031_2D_S3_R1_001
        22.1%
        39.4M
        42.8%
        98.2%
        13.8%
        M004452_M031_3B_S10_R1_001
        20.9%
        37.6M
        43.1%
        98.0%
        13.4%
        M004453_M031_3C_S29_R1_001
        19.5%
        12.4M
        44.3%
        98.4%
        19.3%
        M004465_M031_4G_S23_R1_001
        20.6%
        28.9M
        42.9%
        97.9%
        9.5%
        M004466_M031_4H_S9_R1_001
        18.9%
        29.0M
        43.7%
        98.0%
        15.6%
        M004477_M031_6C_S73_R1_001
        22.2%
        35.2M
        43.0%
        98.1%
        8.9%
        M004479_M031_6E_S71_R1_001
        21.1%
        29.7M
        43.1%
        98.0%
        8.5%
        M004487_M031_7E_S72_R1_001
        21.3%
        29.5M
        43.4%
        97.9%
        9.4%
        M004526_M031_12D_S45_R1_001
        20.8%
        29.6M
        43.2%
        97.8%
        11.6%
        M004955_M036_7E_S94_R1_001
        21.4%
        46.8M
        42.4%
        98.3%
        20.6%
        M004983_M036_11A_S49_R1_001
        18.3%
        47.8M
        42.4%
        98.4%
        34.9%
        M004984_M036_11B_S34_R1_001
        20.5%
        35.0M
        43.2%
        98.3%
        18.4%
        M004989_M036_11G_S48_R1_001
        17.4%
        46.5M
        43.2%
        98.4%
        40.0%
        M005579_M043_1E_S19_R1_001
        20.4%
        22.4M
        42.2%
        97.9%
        12.7%
        M005583_M043_2A_S39_R1_001
        20.3%
        45.7M
        43.3%
        98.3%
        19.0%
        M005592_M043_3B_S40_R1_001
        19.6%
        34.5M
        44.6%
        98.3%
        24.5%
        M005604_M043_4F_S18_R1_001
        20.6%
        27.2M
        43.1%
        97.9%
        9.0%
        M006760_M055_5E_S35_R1_001
        19.1%
        30.2M
        43.4%
        97.9%
        7.8%
        M006764_M055_6A_S36_R1_001
        19.8%
        32.9M
        43.7%
        98.2%
        9.3%
        M006766_M055_6C_S42_R1_001
        19.5%
        33.1M
        43.2%
        97.9%
        13.9%
        M006773_M055_7B_S41_R1_001
        19.2%
        32.5M
        42.4%
        97.9%
        13.3%
        M006800_M055_10E_S47_R1_001
        19.1%
        45.3M
        42.8%
        98.3%
        27.4%
        M006803_M055_10H_S91_R1_001
        21.1%
        31.1M
        44.3%
        98.1%
        10.1%
        M006806_M055_11C_S92_R1_001
        19.6%
        31.5M
        43.0%
        98.0%
        8.5%
        M006807_M055_11D_S93_R1_001
        22.5%
        39.9M
        43.0%
        98.1%
        9.6%
        M007450_M062_7G_S78_R1_001
        20.9%
        27.3M
        43.1%
        97.9%
        6.9%
        M007456_M062_8E_S79_R1_001
        22.9%
        38.9M
        42.9%
        98.1%
        10.5%
        M007591_M064_1D_S16_R1_001
        22.5%
        35.1M
        43.2%
        98.1%
        11.4%
        M007601_M064_2F_S32_R1_001
        20.2%
        25.8M
        42.4%
        98.2%
        15.3%
        M007625_M064_5F_S33_R1_001
        22.0%
        45.8M
        43.2%
        98.4%
        19.6%
        M007630_M064_6C_S28_R1_001
        20.0%
        32.3M
        43.3%
        98.0%
        11.9%
        M007742_M065_8C_S90_R1_001
        21.4%
        31.0M
        43.1%
        97.8%
        6.8%
        M007766_M065_11C_S77_R1_001
        20.4%
        28.4M
        44.1%
        98.2%
        11.8%
        M007878_M067_1C_S76_R1_001
        22.4%
        40.3M
        42.6%
        98.0%
        11.8%
        M007902_M067_4C_S84_R1_001
        21.3%
        36.4M
        42.7%
        98.2%
        11.7%
        M007907_M067_4H_S82_R1_001
        21.6%
        37.8M
        42.7%
        98.1%
        14.7%
        M007908_M067_5A_S83_R1_001
        22.8%
        38.1M
        42.9%
        98.0%
        9.3%
        M076176_M770_1C_S85_R1_001
        21.4%
        41.8M
        42.3%
        98.2%
        20.1%
        M076368_M772_1C_S24_R1_001
        21.0%
        36.9M
        42.4%
        98.2%
        15.5%
        M076372_M772_1G_S12_R1_001
        21.3%
        40.3M
        43.1%
        98.2%
        11.5%
        M076381_M772_2H_S4_R1_001
        21.5%
        33.2M
        43.2%
        98.0%
        7.4%
        M076382_M772_3A_S11_R1_001
        20.8%
        37.6M
        42.6%
        98.0%
        17.0%
        M076692_M775_5G_S86_R1_001
        20.8%
        44.0M
        42.4%
        98.4%
        20.0%
        M076702_M775_7A_S98_R1_001
        21.4%
        43.7M
        42.8%
        98.2%
        19.3%
        M076706_M775_7E_S87_R1_001
        22.5%
        46.3M
        42.9%
        98.3%
        18.2%
        M076712_M775_8C_S99_R1_001
        23.0%
        41.7M
        42.5%
        98.2%
        17.8%
        M076816_M776_9C_S65_R1_001
        21.3%
        33.2M
        42.9%
        98.0%
        11.1%
        M076851_M777_1F_S66_R1_001
        21.7%
        36.7M
        42.6%
        98.1%
        15.3%
        M076891_M777_6F_S81_R1_001
        21.0%
        49.1M
        42.2%
        98.3%
        30.8%
        M076895_M777_7B_S80_R1_001
        20.8%
        39.2M
        42.6%
        98.2%
        19.3%
        M077089_M779_7D_S63_R1_001
        19.1%
        31.0M
        42.8%
        98.0%
        13.5%
        M077113_M779_10D_S46_R1_001
        20.8%
        48.1M
        42.9%
        97.8%
        24.5%
        M077119_M779_11B_S101_R1_001
        23.2%
        49.0M
        43.7%
        98.3%
        14.3%
        M077120_M779_11C_S102_R1_001
        22.2%
        48.7M
        43.8%
        98.4%
        16.8%
        M077920_M789_1D_S64_R1_001
        20.5%
        37.2M
        42.6%
        98.2%
        20.5%
        M077964_M789_6H_S20_R1_001
        21.2%
        38.6M
        42.5%
        98.1%
        14.6%
        M077965_M789_7A_S1_R1_001
        21.0%
        45.9M
        42.5%
        98.4%
        20.2%
        M077975_M789_8C_S21_R1_001
        20.4%
        39.1M
        42.4%
        98.3%
        21.2%
        M077979_M789_8G_S2_R1_001
        20.5%
        41.1M
        42.8%
        98.4%
        21.0%
        M077986_M789_9F_S22_R1_001
        20.6%
        39.3M
        42.5%
        98.3%
        19.9%
        M078007_M789_12C_S31_R1_001
        21.2%
        36.0M
        42.5%
        98.2%
        13.1%
        M078008_M789_12D_S25_R1_001
        20.4%
        35.1M
        42.6%
        98.2%
        14.9%
        M078169_M791_8E_S67_R1_001
        22.0%
        32.7M
        42.7%
        98.0%
        11.0%
        M078686_M797_1B_S5_R1_001
        20.9%
        46.0M
        42.8%
        98.3%
        16.1%
        M078688_M797_1D_S13_R1_001
        20.0%
        43.8M
        43.3%
        98.1%
        18.9%
        M078689_M797_1E_S15_R1_001
        21.6%
        37.5M
        43.0%
        98.2%
        14.1%
        M078692_M797_1H_S6_R1_001
        22.5%
        49.3M
        42.8%
        98.3%
        15.7%
        M078694_M797_2B_S27_R1_001
        22.6%
        43.4M
        42.7%
        98.1%
        16.1%
        M078698_M797_2F_S14_R1_001
        21.8%
        44.3M
        43.3%
        98.3%
        17.3%
        M078711_M797_4C_S26_R1_001
        22.2%
        38.4M
        42.4%
        98.2%
        20.0%
        M078752_M797_9D_S58_R1_001
        21.1%
        39.2M
        43.0%
        98.3%
        20.2%
        M078764_M797_10H_S59_R1_001
        20.4%
        35.4M
        42.8%
        97.8%
        15.5%
        M078766_M797_11B_S95_R1_001
        23.2%
        47.5M
        42.7%
        98.3%
        15.6%
        M078771_M797_11G_S96_R1_001
        21.3%
        47.7M
        42.5%
        98.2%
        24.0%
        M078780_M797_12H_S60_R1_001
        19.7%
        36.3M
        42.8%
        98.1%
        16.5%
        M079054_M800_11B_S38_R1_001
        20.6%
        42.3M
        44.1%
        98.3%
        18.7%
        M079076_M801_1H_S43_R1_001
        20.1%
        34.2M
        43.1%
        98.0%
        11.8%
        M079191_M802_4C_S50_R1_001
        19.7%
        49.6M
        43.0%
        98.3%
        26.5%
        M079205_M802_6A_S51_R1_001
        19.3%
        27.7M
        43.0%
        97.5%
        5.9%
        M079248_M802_11D_S56_R1_001
        22.0%
        33.5M
        43.5%
        98.1%
        8.0%
        M079251_M802_11G_S57_R1_001
        21.5%
        43.1M
        42.5%
        98.3%
        21.5%
        M079258_M802_12F_S55_R1_001
        20.8%
        37.9M
        42.4%
        98.2%
        19.2%
        M079477_M805_4A_S100_R1_001
        21.4%
        33.2M
        42.9%
        97.9%
        8.1%
        M079484_M805_4H_S69_R1_001
        21.0%
        34.0M
        42.9%
        98.0%
        8.6%
        M079485_M805_5A_S70_R1_001
        20.9%
        36.2M
        42.6%
        98.0%
        12.3%
        M079547_M805_12G_S68_R1_001
        22.0%
        41.1M
        42.7%
        98.1%
        13.7%
        M079946_M810_2F_S53_R1_001
        18.4%
        53.4M
        42.3%
        98.3%
        37.9%
        M079957_M810_4A_S52_R1_001
        20.0%
        48.1M
        43.4%
        98.2%
        26.4%
        M080026_M810_12F_S54_R1_001
        20.0%
        43.6M
        42.1%
        98.3%
        24.2%
        M086592_M879_7E_S88_R1_001
        22.8%
        44.6M
        42.6%
        98.3%
        15.6%
        M086603_M879_8H_S89_R1_001
        19.9%
        44.8M
        42.3%
        98.2%
        25.2%
        M086735_M881_1D_S97_R1_001
        21.5%
        42.3M
        42.9%
        98.3%
        16.3%
        M086769_M881_5F_S8_R1_001
        20.4%
        34.1M
        43.2%
        98.2%
        15.4%
        M086773_M881_6B_S7_R1_001
        23.0%
        39.5M
        43.1%
        98.2%
        12.4%
        M086813_M881_11B_S17_R1_001
        20.9%
        31.9M
        43.0%
        98.2%
        12.6%
        M086821_M881_12B_S37_R1_001
        21.0%
        51.4M
        42.6%
        98.3%
        21.1%
        M086826_M881_12G_S44_R1_001
        20.7%
        37.0M
        41.8%
        97.1%
        23.8%

        fastp

        Version: 0.23.4

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).DOI: 10.1093/bioinformatics/bty560.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        fastp0.23.4